We investigate system identification for general quantum linear systems in the situation where the input field is prepared as stationary (squeezed) quantum noise. In this regime the output field is characterised by the power spectrum, which encodes covariance of the output state. We address which parameters can be identified from the power spectrum and how to construct a system realisation from the power spectrum. The power spectrum depends on the system parameters via the transfer function. We show that the transfer function can be uniquely recovered from the power spectrum, so that equivalent systems are related by a symplectic transformation. Crown Copyright (C) 2018 Published by Elsevier Ltd. All rights reserved.